Dannon Baker
1e0d76526c
Config rebuild for registration message update.
2025-02-12 07:55:59 -05:00
John Davis
54fc956cca
Add documentation on handling a deadlock error during db migration
2025-02-05 15:03:33 -05:00
Dannon Baker
e858bf01a2
Make config-rebuild
2024-11-18 20:42:12 -05:00
Dannon Baker
944ac9c786
Make openai key configurable
2024-11-18 09:11:20 -05:00
Marius van den Beek
9b39ec7ef3
Merge pull request #18996 from martenson/schema-cond
2024-11-01 03:43:13 -04:00
Nicola Soranzo
93078d949a
Replace poetry with uv
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for lightning-fast Python dependency updates.
To update all dependencies (as done by the GitHub action):
$ make update-dependencies
To update only one package:
./lib/galaxy/dependencies/update.sh -p <PKG>
2024-10-31 10:22:52 +00:00
Nate Coraor
d622d2d8f1
Remove conda_auto_init default from schema as suggested
2024-10-28 14:50:01 -04:00
Nate Coraor
90caa402a5
Disable conda_auto_init default = true when not running from source
2024-10-24 10:05:41 -04:00
Martin Cech
c6ead00287
run make config-revuild
2024-10-15 12:03:25 +02:00
John Chilton
edc5bc2a8f
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
Sanjay Srikakulam
22863a1ccb
Add new config parameter for file sources temp dir and update the webdav file source
2024-10-10 10:44:40 +00:00
Sanjay Srikakulam
3d28b2b9c9
remove use_temp_files configuration parameter
2024-10-10 10:40:58 +00:00
Sanjay Srikakulam
1c9c33ee8d
lint fix
2024-10-10 10:40:58 +00:00
Sanjay Srikakulam
2ca28420fe
Add images of the webdav conf and template and update file source templates image
2024-10-10 10:40:58 +00:00
Sanjay Kumar Srikakulam
83eabbe054
lint fix
2024-10-10 10:40:58 +00:00
Sanjay Kumar Srikakulam
22791a8d43
Add WebDAV as user file source
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Adds WebDAV example template, configuration and updates the docs, and the file source model along with the client API schema
2024-10-10 10:40:58 +00:00
John Chilton
ab70b5be6a
Rebuild schema...
2024-10-05 17:23:26 -04:00
John Davis
d0d0838c51
Merge pull request #18481 from kysrpex/interactivetoolssqlalchemy
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Support high-availability setups for the interactive tools proxy
2024-09-04 18:04:53 -04:00
José Manuel Domínguez
9ee6636f4a
Rename interactivetools_map_sqlalchemy to interactivetoolsproxy_map
2024-09-03 14:17:12 +02:00
Nicola Soranzo
c778a2ae3f
Remove conda defaults channel from more places
2024-09-02 14:03:18 +01:00
José Manuel Domínguez and John Davis
018e5417c2
Mention that interactivetools_map_sqlalchemy overrides interactivetools_map in the latter's description
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Co-authored-by: John Davis <jdavcs@gmail.com >
2024-08-09 09:58:30 +02:00
José Manuel Domínguez
ffa8ea4f4d
Fix typos in descriptions of interactivetools_map and interactivetools_map_sqlalchemy
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Authored-by: John Davis <jdavcs@gmail.com >
2024-08-09 09:42:30 +02:00
José Manuel Domínguez
c1fd2b569b
Merge branch 'dev' into interactivetoolssqlalchemy
2024-07-23 12:19:58 +02:00
José Manuel Domínguez
dddf5ba9f6
Add note in interactive tools docs page informing about interactivetools_map_sqlalchemy setting
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Refer to SQLite docs page describing situations where a client/server RDBMS works better and provide an example. Link to the `interactivetools_map_sqlalchemy` on the Galaxy configuration page.
2024-07-22 17:22:25 +02:00
José Manuel Domínguez
ce6d0f73c5
Configure SQLAlchemy interactive tool maps via new interactivetools_map_sqlalchemy setting
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Define a new configuration property `interactivetools_map_sqlalchemy` to store interactivetool proxy mappings on a RDBMS supported by SQLAlchemy.
If set, it takes precedence over `interactivetools_map`. When unset, a SQLite mapping file located at `interactivetools_map` is used (as usual).
2024-07-22 17:22:24 +02:00
Marius van den Beek
a7fb571143
Merge pull request #18499 from bgruening/obs_cache_size
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small docs enhancement
2024-07-11 11:33:32 +02:00
Martin Cech
7264a82589
regenerate config sample and docs
2024-07-05 09:19:40 -07:00
Björn Grüning
3724309809
small docs enhancement
2024-07-05 10:46:44 +02:00
José Manuel Domínguez
967b59140e
Merge branch 'refs/heads/dev' into interactivetoolssqlalchemy
2024-07-04 13:52:59 +02:00
José Manuel Domínguez
b54bf35518
Support using a table in any database supported by SQLAlchemy as mapping for interactive tools
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Replace the class `InteractiveToolSqlite` in lib/galaxy/managers/interactivetool.py with a new class `InteractiveToolPropagatorSQLAlchemy`. The new class implements a SQLAlchemy "propagator" for `InteractiveToolManager` (on the same file). This propagator writes the mappings to the table named after the value of `DATABASE_TABLE_NAME`, in the database specified by the SQLAlchemy database url passed to its constructor. Change the constructor of `InteractiveToolManager` so that it uses `InteractiveToolPropagatorSQLAlchemy`.
Change the method `_process_config` of `galaxy.config.GalaxyAppConfiguration` so that it converts the value of `interactivetools_map` to a SQLAlchemy database url if it is a path.
Update documentation to reflect these changes.
2024-07-02 11:24:34 +02:00
Dannon Baker
6ec7521e1a
Merge remote-tracking branch 'upstream/release_24.0' into release_24.1
2024-06-28 09:48:27 +02:00
mvdbeek
7c6fc1800f
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
Bjoern Gruening
5eec5cc7ae
rebuild Galaxy config
2024-06-04 21:30:24 +02:00
John Chilton
b598bff3e0
Big warning box about distributed object stores being required.
2024-05-20 12:19:01 -04:00
John Chilton
29ea0ba522
Implement many PR comments around Vue stuff and docs.
2024-05-20 12:19:01 -04:00
John Chilton
f95da89b3d
Implement file source templates
2024-05-20 12:18:47 -04:00
John Davis
076f298a99
Merge pull request #18079 from jdavcs/dev_userless_history_script_and_tests
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Script for deleting userless histories from database + testing + drop unused model testing code
2024-05-14 13:48:24 -04:00
John Davis
3904681f40
Provide an example of ISO format
2024-05-14 13:47:35 -04:00
John Davis
77d8d61e90
Add documentation
2024-05-13 22:17:21 -04:00
John Davis
54bb8a9a06
Fix bug in admin/container docs section title markup
2024-05-13 21:03:39 -04:00
tianzedavid
04bfa209e7
chore: remove repetitive words
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Signed-off-by: tianzedavid <cuitianze@aliyun.com >
2024-05-02 21:30:03 +08:00
Nicola Soranzo
1d64120a00
Merge branch 'release_24.0' into dev
2024-04-25 14:32:52 +01:00
mvdbeek
f26e90f712
Log start and end of request
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Configurable via `use_access_logging_middleware`.
Looks like this:
```
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:43,776 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:48,719 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435 200
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,767 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,786 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4 200
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:53,139 [pN:main,p:73562,tN:MainThread] GET /api/entry_points?running=true 763693e9-4fd3-4a97-a100-a3c259b4b4c8
```
2024-04-24 17:08:06 +02:00
Martin Cech
ffc66f2c28
Merge pull request #17585 from bernt-matthias/admin-doc-data-tables
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Add some admin facing docs on data tables
2024-04-18 18:55:55 +02:00
Martin Cech
abad770d5a
change text in a minor way
2024-04-18 18:55:38 +02:00
davelopez
dbdd5bca81
Add dispatch_notifications_interval config option
2024-04-16 17:06:19 +02:00
davelopez and Nicola Soranzo
3bb49cab8e
Move result_backend comment to celery_conf
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Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk >
2024-04-11 09:21:27 +02:00
davelopez
514df55323
Add broker and backend defaults as null
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This will keep the values in the sample config.
2024-04-10 18:23:52 +02:00
davelopez
a739ed1cb8
Rebuild config samples
2024-04-10 17:56:52 +02:00
davelopez and Nicola Soranzo
4ec8cef337
Reword sentence
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Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk >
2024-04-10 17:03:55 +02:00
Dannon Baker